diff --git a/vignettes/epidist.Rmd b/vignettes/epidist.Rmd index 7edf55fc3..86fa9b254 100644 --- a/vignettes/epidist.Rmd +++ b/vignettes/epidist.Rmd @@ -288,13 +288,8 @@ In particular, we use the the No-U-Turn Sampler (NUTS) Markov chain Monte Carlo fit <- epidist(data = data, chains = 2, cores = 2, refresh = 0) ``` -The `fit` object is a `brmsfit` object containing MCMC samples from each of the parameters (Table \@ref(tab:pars)) in the model. -Users familiar with Stan and `brms`, can work with `fit` directly. -Any tool that supports `brms` fitted model objects will be compatible with `fit`. - -**Note that here we use the default `rstan` backend but we generally recommend using the `cmdstanr` backend for faster sampling and additional features. This can be set using `backend = "cmdstanr"` after following the installing `cmdstan` instructions in the README.** - -(ref:pars) All of the parameters that are included in the model. Many of these parameters (e.g. `swindow` and `pwindow`) are the so called latent variables in the model, and have lengths corresponding to the `sample_size`. We extracted the model parameters using `brms::variables()` and removed the indices. +The `fit` object is a `brmsfit` object containing MCMC samples from each of the parameters in the model, shown in the table below. +Many of these parameters (e.g. `swindow` and `pwindow`) are the so called latent variables, and have lengths corresponding to the `sample_size`. ```{r pars} pars <- fit |> @@ -304,10 +299,15 @@ pars <- fit |> data.frame( Parameter = unique(pars), Length = table(pars) ) |> - gt() |> - tab_caption("(ref:pars)") + gt() ``` +Users familiar with Stan and `brms`, can work with `fit` directly. +Any tool that supports `brms` fitted model objects will be compatible with `fit`. + +**Note that here we use the default `rstan` backend but we generally recommend using the `cmdstanr` backend for faster sampling and additional features.** +**This can be set using `backend = "cmdstanr"` after following the installing CmdStan instructions in the README.** + The `epidist` package also provides functions to make common post-processing tasks easy. For example, individual predictions of the lognormal delay parameters can be extracted using: